diff --git a/examples/react/src/examples/UseNodesInit/index.tsx b/examples/react/src/examples/UseNodesInit/index.tsx
index 549315ca..d4932ae1 100644
--- a/examples/react/src/examples/UseNodesInit/index.tsx
+++ b/examples/react/src/examples/UseNodesInit/index.tsx
@@ -11,6 +11,8 @@ import {
   useEdgesState,
   OnConnect,
   useNodesInitialized,
+  Panel,
+  useReactFlow,
 } from '@xyflow/react';
 
 const initialNodes: Node[] = [
@@ -49,6 +51,7 @@ const initialEdges: Edge[] = [
 ];
 
 const UseZoomPanHelperFlow = () => {
+  const { addNodes } = useReactFlow();
   const [nodes, setNodes, onNodesChange] = useNodesState(initialNodes);
   const [edges, setEdges, onEdgesChange] = useEdgesState(initialEdges);
 
@@ -59,6 +62,13 @@ const UseZoomPanHelperFlow = () => {
     console.log('initialized', initialized);
   }, [initialized]);
 
+  const addNode = () =>
+    addNodes({
+      id: `${Math.random()}`,
+      data: { label: 'new node' },
+      position: { x: Math.random() * 400, y: Math.random() * 400 },
+    });
+
   return (
     <ReactFlow
       nodes={nodes}
@@ -71,6 +81,9 @@ const UseZoomPanHelperFlow = () => {
     >
       <Background />
       <MiniMap />
+      <Panel>
+        <button onClick={addNode}>add node</button>
+      </Panel>
     </ReactFlow>
   );
 };
diff --git a/packages/react/src/hooks/useReactFlow.ts b/packages/react/src/hooks/useReactFlow.ts
index 4ac0e50c..a61d4907 100644
--- a/packages/react/src/hooks/useReactFlow.ts
+++ b/packages/react/src/hooks/useReactFlow.ts
@@ -1,9 +1,11 @@
 import { useCallback, useMemo } from 'react';
 import {
+  EdgeRemoveChange,
   evaluateAbsolutePosition,
   getElementsToRemove,
   getOverlappingArea,
   isRectObject,
+  NodeRemoveChange,
   nodeToRect,
   type Rect,
 } from '@xyflow/system';
@@ -11,7 +13,7 @@ import {
 import useViewportHelper from './useViewportHelper';
 import { useStoreApi } from './useStore';
 import { useBatchContext } from '../components/BatchProvider';
-import { isNode } from '../utils';
+import { elementToRemoveChange, isNode } from '../utils';
 import type { ReactFlowInstance, Instance, Node, Edge, InternalNode } from '../types';
 
 /**
@@ -87,12 +89,10 @@ export function useReactFlow<NodeType extends Node = Node, EdgeType extends Edge
       const {
         nodes,
         edges,
-        hasDefaultNodes,
-        hasDefaultEdges,
         onNodesDelete,
         onEdgesDelete,
-        onNodesChange,
-        onEdgesChange,
+        triggerNodeChanges,
+        triggerEdgeChanges,
         onDelete,
         onBeforeDelete,
       } = store.getState();
@@ -108,28 +108,17 @@ export function useReactFlow<NodeType extends Node = Node, EdgeType extends Edge
       const hasMatchingNodes = matchingNodes.length > 0;
 
       if (hasMatchingEdges) {
-        if (hasDefaultEdges) {
-          const nextEdges = edges.filter((e) => !matchingEdges.some((mE) => mE.id === e.id));
-          store.getState().setEdges(nextEdges);
-        }
+        const edgeChanges: EdgeRemoveChange[] = matchingEdges.map(elementToRemoveChange);
 
         onEdgesDelete?.(matchingEdges);
-        onEdgesChange?.(
-          matchingEdges.map((edge) => ({
-            id: edge.id,
-            type: 'remove',
-          }))
-        );
+        triggerEdgeChanges(edgeChanges);
       }
 
       if (hasMatchingNodes) {
-        if (hasDefaultNodes) {
-          const nextNodes = nodes.filter((n) => !matchingNodes.some((mN) => mN.id === n.id));
-          store.getState().setNodes(nextNodes);
-        }
+        const nodeChanges: NodeRemoveChange[] = matchingNodes.map(elementToRemoveChange);
 
         onNodesDelete?.(matchingNodes);
-        onNodesChange?.(matchingNodes.map((node) => ({ id: node.id, type: 'remove' })));
+        triggerNodeChanges(nodeChanges);
       }
 
       if (hasMatchingNodes || hasMatchingEdges) {
diff --git a/packages/react/src/store/index.ts b/packages/react/src/store/index.ts
index 5d7f521b..29f99999 100644
--- a/packages/react/src/store/index.ts
+++ b/packages/react/src/store/index.ts
@@ -74,7 +74,7 @@ const createStore = ({
       // new dimensions and update the nodes.
       updateNodeInternals: (updates) => {
         const {
-          onNodesChange,
+          triggerNodeChanges,
           fitView,
           nodeLookup,
           parentLookup,
@@ -120,7 +120,7 @@ const createStore = ({
           if (debug) {
             console.log('React Flow: trigger node changes', changes);
           }
-          onNodesChange?.(changes);
+          triggerNodeChanges?.(changes);
         }
       },
       updateNodePositions: (nodeDragItems, dragging = false) => {
diff --git a/packages/react/src/utils/changes.ts b/packages/react/src/utils/changes.ts
index cdc83088..df215340 100644
--- a/packages/react/src/utils/changes.ts
+++ b/packages/react/src/utils/changes.ts
@@ -6,6 +6,8 @@ import {
   NodeChange,
   NodeSelectionChange,
   EdgeSelectionChange,
+  NodeRemoveChange,
+  EdgeRemoveChange,
 } from '@xyflow/system';
 import type { Node, Edge, InternalNode } from '../types';
 
@@ -258,3 +260,10 @@ export function getElementsDiffChanges({
 
   return changes;
 }
+
+export function elementToRemoveChange<T extends Node | Edge>(item: T): NodeRemoveChange | EdgeRemoveChange {
+  return {
+    id: item.id,
+    type: 'remove',
+  };
+}
diff --git a/packages/system/src/utils/graph.ts b/packages/system/src/utils/graph.ts
index 53592609..6a4715b8 100644
--- a/packages/system/src/utils/graph.ts
+++ b/packages/system/src/utils/graph.ts
@@ -395,7 +395,7 @@ export async function getElementsToRemove<NodeType extends NodeBase = NodeBase,
   nodes: NodeType[];
   edges: EdgeType[];
 }> {
-  const nodeIds = nodesToRemove.map((node) => node.id);
+  const nodeIds = new Set(nodesToRemove.map((node) => node.id));
   const matchingNodes: NodeType[] = [];
 
   for (const node of nodes) {
@@ -403,7 +403,7 @@ export async function getElementsToRemove<NodeType extends NodeBase = NodeBase,
       continue;
     }
 
-    const isIncluded = nodeIds.includes(node.id);
+    const isIncluded = nodeIds.has(node.id);
     const parentHit = !isIncluded && node.parentId && matchingNodes.find((n) => n.id === node.parentId);
 
     if (isIncluded || parentHit) {
@@ -411,13 +411,13 @@ export async function getElementsToRemove<NodeType extends NodeBase = NodeBase,
     }
   }
 
-  const edgeIds = edgesToRemove.map((edge) => edge.id);
+  const edgeIds = new Set(edgesToRemove.map((edge) => edge.id));
   const deletableEdges = edges.filter((edge) => edge.deletable !== false);
   const connectedEdges = getConnectedEdges(matchingNodes, deletableEdges);
   const matchingEdges: EdgeType[] = connectedEdges;
 
   for (const edge of deletableEdges) {
-    const isIncluded = edgeIds.includes(edge.id);
+    const isIncluded = edgeIds.has(edge.id);
 
     if (isIncluded && !matchingEdges.find((e) => e.id === edge.id)) {
       matchingEdges.push(edge);